Re: [Rdkit-discuss] sanitization removes Hs - is this expected?

[Michal K. <mic...@gm...>]

Thanks a lot!
By the way, it would be useful to have this feature (MergeQueryHs) also in
the substructure search KNIME node.
Best wishes,
Michal
On 3 April 2015 at 06:29, Greg Landrum <gre...@gm...> wrote:

> The changes are now pushed (
> https://github.com/rdkit/rdkit/commit/f0d4cf1ec63a4928a2a28fa62cf1d255099e72d0)
> and are available on master.
> The new functions are qmol_from_smiles() and qmol_from_ctab()
>
> Best,
> -greg
>
>
> On Thu, Apr 2, 2015 at 10:51 AM, Greg Landrum <gre...@gm...>
> wrote:
>
>> Hi Michal,
>>
>> Glad to hear this matches what you are looking for. I have already added
>> the feature to the cartridge and will check it in later today/tomorrow
>> morning.
>>
>> -greg
>>
>> On Thursday, April 2, 2015, Michal Krompiec <mic...@gm...>
>> wrote:
>>
>>>  Hi Greg,
>>> Thank you, this is exactly what I needed.
>>>
>>> On 2 April 2015 at 05:22, Greg Landrum <gre...@gm...> wrote:
>>>
>>>>
>>>> Skipping sanitization, as you propose, isn't going to help here: the
>>>> kekulized form of the ring will not be converted to aromatic and you won't
>>>> get the matches you are looking for.
>>>>
>>> Indeed. Previously I stored my dataset as smiles with explicit
>>> hydrogens, and created the query mols by adding Hs and then deleting
>>> hydrogens at substitution sites and finally converting to SMARTS - a messy
>>> workaround, but producing the right result.
>>>
>>>
>>>>   Here's an approach to this that works in Python :
>>>>
>>>
>>>
>>> And this is exactly what I wanted. To illustrate it more precisely: your
>>> pattern (2-H-pyrimidine) matches pyrimidine, 5-methylpyrimidine but does
>>> not match 2-pyrimidine:
>>>
>>> >>> m =Chem.MolFromSmiles('c1ccnc([H])n1',sanitize=False);
>>> >>> nm=Chem.MergeQueryHs(m)
>>> >>> Chem.SanitizeMol(nm)
>>> rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
>>> >>> Chem.MolFromSmiles('c1ccncn1').HasSubstructMatch(nm)
>>> True
>>> >>> Chem.MolFromSmiles('c1c(C)cncn1').HasSubstructMatch(nm)
>>> True
>>> >>> Chem.MolFromSmiles('c1ccnc(C)n1').HasSubstructMatch(nm)
>>> False
>>> >>>
>>>
>>>
>>>
>>>>
>>>>  Being able to do something equivalent in the cartridge would
>>>> certainly be useful. What I'd suggest is the addition of two functions:
>>>> "query_mol_from_smiles()" and "query_mol_from_ctab()" that do this.
>>>>
>>>
>>> I'll do it.
>>>
>>>
>>>   Then you could do queries like:
>>>> select * from mols where m @> query_mol_from_smiles('c1ccnc([H])n1');
>>>> and have it do the right thing.
>>>>
>>>> Sound reasonable?
>>>>
>>>> -greg
>>>>
>>>>
>>> Best wishes,
>>> Michal
>>>
>>>
>